How can I make transparency act as expected with the internal renderer?
The main problem is anti-aliasing the alpha borders of the leaves. You should enable Full Sample in the Render options for best quality. This will render correctly:



Other problem for best quality might be the transparent texture itself. There is no color bleed over the transparent edge. There is black background over the transparent pixels.
On the leafs texture sampling and filtering happens. And the transparent border get's blurred and the black leaks into the leafs. The image without alpha channel should look like the right one:



Make sure when you are exporting the whole rgb channels are exported and not clipped with the alpha channel.